Crystal structure of a putative dyp-type peroxidase protein (so_0740) from shewanella oneidensis at 2.75 A resolution

Experimental Data Snapshot

  • Resolution: 2.75 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif.

Zubieta, C.Krishna, S.S.Kapoor, M.Kozbial, P.McMullan, D.Axelrod, H.L.Miller, M.D.Abdubek, P.Ambing, E.Astakhova, T.Carlton, D.Chiu, H.J.Clayton, T.Deller, M.C.Duan, L.Elsliger, M.A.Feuerhelm, J.Grzechnik, S.K.Hale, J.Hampton, E.Han, G.W.Jaroszewski, L.Jin, K.K.Klock, H.E.Knuth, M.W.Kumar, A.Marciano, D.Morse, A.T.Nigoghossian, E.Okach, L.Oommachen, S.Reyes, R.Rife, C.L.Schimmel, P.van den Bedem, H.Weekes, D.White, A.Xu, Q.Hodgson, K.O.Wooley, J.Deacon, A.M.Godzik, A.Lesley, S.A.Wilson, I.A.

(2007) Proteins 69: 223-233

  • DOI: https://doi.org/10.1002/prot.21550
  • Primary Citation of Related Structures:  
    2GVK, 2HAG

  • PubMed Abstract: 

    BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are dye-decolorizing peroxidases (DyPs), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 A, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two-domain, alpha+beta ferredoxin-like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme-binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein).

  • Organizational Affiliation

    Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Melanin biosynthesis protein TyrA, putative312Shewanella oneidensisMutation(s): 13 
Gene Names: np_716371.1
Find proteins for Q8EIU4 (Shewanella oneidensis (strain MR-1))
Explore Q8EIU4 
Go to UniProtKB:  Q8EIU4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EIU4
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.31α = 90
b = 94.31β = 90
c = 113.68γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-01-25
    Changes: Database references, Derived calculations